Non-Coding Transcriptome Provides Novel Insights into the Escherichia coli F17 Susceptibility of Sheep Lamb

Abstract

It has long been recognized that enterotoxigenic Escherichia coli (ETEC) is the major pathogen responsible for vomiting and diarrhea. E. coli F17, a main subtype of ETEC, is characterized by high morbidity and mortality in young livestock. However, the transcriptomic basis underlying E. coli F17 infection has not been fully understood. In this study, RNA sequencing was performed to explore the expression profiles of circRNAs and miRNAs in the jejunum of E. coli F17-antagonism (AN) and -sensitive (SE) lambs. A total of 16,534 circRNAs and 271 miRNAs (125 novel miRNAs and 146 annotated miRNAs) were screened, and 214 differentially expressed (DE) circRNAs and 53 DE miRNAs were detected between the AN and SE lambs (i.e., novel_circ_0025840, novel_circ_0022779, novel_miR_107, miR-10b). Functional enrichment analyses showed that source genes of DE circRNAs were mainly involved in metabolic-related pathways, while target genes of DE miRNAs were mainly enriched in the immune response pathways. Then, a two-step machine learning approach combining Random Forest (RF) and XGBoost (candidates were first selected by RF and further assessed by XGBoost) was performed, which identified 44 circRNAs and 39 miRNAs as potential biomarkers (i.e., novel_circ_0000180, novel_circ_0000365, novel_miR_192, oar-miR-496-3p) for E. coli infection. Furthermore, circRNA-related and lncRNA-related ceRNA networks were constructed, containing 46 circRNA-miRNA-mRNA competing triplets and 630 lncRNA-miRNA-mRNA competing triplets, respectively. By conducting a serious of bioinformatic analyses, our results revealed important circRNAs and miRNAs that could be potentially developed as candidate biomarkers for intestinal inflammatory response against E. coli F17 infection; our study can provide novel insights into the underlying mechanisms of intestinal immunity.

A Study of the Resistance of Hu Sheep Lambs to Escherichia coli F17 Based on Whole Genome Sequencing

“…The rapid spread of sheep diseases has led to an increase in the culling of sheep and losses to breeding farms. Escherichia coli infections are a major threat to young animals and can be fatal in severe cases [ 51 , 52 ]. Therefore, the breeding of high quality disease-resistant sheep is an important issue, and the use of key genes or candidate sites that influence the occurrence of sheep diseases can improve the economic benefits of breeding enterprises and promote the healthy development of the sheep industry.…”

miR-329b-5p Affects Sheep Intestinal Epithelial Cells against Escherichia coli F17 Infection

“…A. Jaeger et al found that many miRNAs were significantly up-regulated in porcine mammary epithelial cells attacked for 3 and 24 h [44]. Chen et al conducted RNA sequencing on the ileal tissues of sheep that were either E. coli F17-sensitive or antagonistic, identifying differentially expressed miRNAs and circRNAs, and constructing the corresponding ceRNA networks [45]. Therefore, in this study, we selected the screened differentially expressed miR-329b-5p to investigate the role of miRNAs against E. coli infection in sheep.…”

Non-coding transcriptomic profiles in the sheep mammary gland during different lactation periods

“…Previously, we compared the classification accuracy of several decision tree-based machine learning approaches (Random Forest, XGBoost, and RX) and DE transcript identification methods (edgeR and t -test) in subsets of transcriptomic data. The results showed that a method combining Random Forest and XGBoost (RX) outperformed the other four methods (Random Forest, XGBoost, t -test, and edgeR) with the highest classification accuracy and showed biological value in the prediction of multiple traits such as feed efficiency ( 26 ) and Escherichia coli infection ( 60 ).…”